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Bioinformatics Advance Access originally published online on March 15, 2005
Bioinformatics 2005 21(10):2520-2521; doi:10.1093/bioinformatics/bti380
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

MIPS bacterial genomes functional annotation benchmark dataset

Igor V. Tetko *, Barbara Brauner , Irmtraud Dunger-Kaltenbach , Goar Frishman , Corinna Montrone , Gisela Fobo , Andreas Ruepp , Alexey V. Antonov , Dimitrij Surmeli and Hans-Wernen Mewes

Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany

*To whom correspondence should be addressed.

Motivation: Any development of new methods for automatic functional annotation of proteins according to their sequences requires high-quality data (as benchmark) as well as tedious preparatory work to generate sequence parameters required as input data for the machine learning methods. Different program settings and incompatible protocols make a comparison of the analyzed methods difficult.

Results: The MIPS Bacterial Functional Annotation Benchmark dataset (MIPS-BFAB) is a new, high-quality resource comprising four bacterial genomes manually annotated according to the MIPS functional catalogue (FunCat). These resources include precalculated sequence parameters, such as sequence similarity scores, InterPro domain composition and other parameters that could be used to develop and benchmark methods for functional annotation of bacterial protein sequences. These data are provided in XML format and can be used by scientists who are not necessarily experts in genome annotation.

Availability: BFAB is available at http://mips.gsf.de/proj/bfab

Contact: i.tetko{at}gsf.de


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